title: Novel Conserved Genotypes Correspond to Antibiotic Resistance Phenotypes of E. coli Clinical Isolates.
abstract: Current efforts to understand antibiotic resistance on the whole genome scale tend to focus on known genes even as high throughput sequencing strategies uncover novel mechanisms. To identify genomic variations associated with antibiotic resistance, we employed a modified genome-wide association study; we sequenced genomic DNA from pools of E. coli clinical isolates with similar antibiotic resistance phenotypes using SOLiD technology to uncover single nucleotide polymorphisms (SNPs) unanimously conserved in each pool. The multidrug-resistant pools were genotypically similar to SMS-3-5, a previously sequenced multidrug-resistant isolate from a polluted environment. The similarity was evenly spread across the entire genome and not limited to plasmid or pathogenicity island loci. Among the pools of clinical isolates, genomic variation was concentrated adjacent to previously reported inversion and duplication differences between the SMS-3-5 isolate and the drug-susceptible laboratory strain, DH10B. SNPs that result in non-synonymous changes in gyrA (encoding the well-known S83L allele associated with fluoroquinolone resistance), mutM, ligB, and recG were unanimously conserved in every fluoroquinolone-resistant pool. Alleles of the latter three genes are tightly linked among most sequenced E. coli genomes, and had not been implicated in antibiotic resistance previously. The changes in these genes map to amino acid positions in alpha helices that are involved in DNA binding. Plasmid-encoded complementation of null strains with either allelic variant of mutM or ligB resulted in variable responses to ultraviolet light or hydrogen peroxide treatment as markers of induced DNA damage, indicating their importance in DNA metabolism and revealing a potential mechanism for fluoroquinolone resistance. Our approach uncovered evidence that additional DNA binding enzymes may contribute to fluoroquinolone resistance and further implicate environmental bacteria as a reservoir for antibiotic resistance.
authors.affiliation: Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America ; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America.
authors.forename: Michelle C
authors.initials: MC
authors.lastname: Swick
authors.forename: Michael A
authors.initials: MA
authors.lastname: Evangelista
authors.forename: Truston J
authors.initials: TJ
authors.lastname: Bodine
authors.forename: Jeremy R
authors.initials: JR
authors.lastname: Easton-Marks
authors.forename: Patrick
authors.initials: P
authors.lastname: Barth
authors.forename: Minita J
authors.initials: MJ
authors.lastname: Shah
authors.forename: Christina A
authors.initials: CA
authors.lastname: Bormann Chung
authors.forename: Sarah
authors.initials: S
authors.lastname: Stanley
authors.forename: Stephen F
authors.initials: SF
authors.lastname: McLaughlin
authors.forename: Clarence C
authors.initials: CC
authors.lastname: Lee
authors.forename: Vrunda
authors.initials: V
authors.lastname: Sheth
authors.forename: Quynh
authors.initials: Q
authors.lastname: Doan
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Hamill
authors.forename: David
authors.initials: D
authors.lastname: Steffen
authors.forename: Lauren B
authors.initials: LB
authors.lastname: Becnel
authors.forename: Richard
authors.initials: R
authors.lastname: Sucgang
authors.forename: Lynn
authors.initials: L
authors.lastname: Zechiedrich
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D004269:DNA, Bacterial / Q000235:genetics; D024881:Drug Resistance, Bacterial / Q000235:genetics*; D004926:Escherichia coli / Q000187:drug effects* / Q000235:genetics; D024841:Fluoroquinolones / Q000494:pharmacology*; D005838:Genotype; D008826:Microbial Sensitivity Tests; D020641:Polymorphism, Single Nucleotide
chemical_list: D000900:Anti-Bacterial Agents; D004269:DNA, Bacterial; D024841:Fluoroquinolones